Contacts of the helix formed by residues 168 - 182 (chain A) in PDB entry 1M1B
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with GLY 168 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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162A ALA* 4.6 0.9 - - - +
163A PHE* 3.8 8.3 - - - -
167A TRP* 1.3 81.5 - - - +
169A LEU* 1.3 64.6 + - - -
170A ASP 3.5 2.2 - - - -
171A GLU* 3.7 6.3 - - - +
172A ALA* 3.3 20.4 + - - +
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Residues in contact with LEU 169 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163A PHE* 3.8 21.8 - - + -
168A GLY* 1.3 68.5 - - - -
170A ASP* 1.3 63.7 + - - +
171A GLU 3.2 1.6 - - - -
172A ALA 3.1 1.2 + - - -
173A LEU* 2.7 41.6 + - + +
201A ALA* 3.8 23.6 - - + +
202A PHE* 3.7 31.6 - - + +
205A ALA* 4.1 17.7 - - + -
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Residues in contact with ASP 170 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168A GLY 3.5 0.4 - - - -
169A LEU* 1.3 82.2 - - - +
171A GLU* 1.3 53.3 + - - +
173A LEU* 3.8 10.1 - - - +
174A LYS* 2.8 47.7 + - - +
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Residues in contact with GLU 171 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132A LEU* 3.7 11.4 - - - +
135A ILE* 4.0 9.0 - - - +
162A ALA* 4.3 1.8 - - + +
167A TRP* 3.9 33.9 - - + -
168A GLY* 3.7 12.7 + - - +
169A LEU 3.2 0.6 - - - -
170A ASP* 1.3 76.3 - - - +
172A ALA* 1.3 60.3 + - - +
174A LYS* 3.1 15.8 + - - +
175A ARG* 2.7 81.5 + - - +
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Residues in contact with ALA 172 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160A VAL* 3.7 12.9 - - + +
162A ALA* 3.6 20.8 - - + +
163A PHE* 3.7 33.7 - - + -
168A GLY 3.3 7.3 + - - +
169A LEU* 3.1 8.6 + - + +
171A GLU* 1.3 78.4 - - - +
173A LEU* 1.3 59.9 + - - +
175A ARG* 3.2 2.6 + - - +
176A ALA* 2.9 30.1 + - - +
189A MET* 4.0 7.1 - - + +
202A PHE* 5.0 1.1 - - + -
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Residues in contact with LEU 173 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169A LEU* 2.7 29.7 + - + +
170A ASP* 3.8 8.5 - - - +
172A ALA* 1.3 73.6 - - - +
174A LYS* 1.3 63.9 + - - +
176A ALA* 3.7 0.2 - - - +
177A GLU* 3.1 50.3 + - - +
202A PHE* 4.2 13.4 - - + -
205A ALA* 3.9 39.7 - - + +
206A TRP* 4.2 19.7 - - + -
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Residues in contact with LYS 174 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135A ILE* 3.8 22.2 - - + -
170A ASP* 2.8 31.5 + - - +
171A GLU* 3.3 16.4 - - - +
173A LEU* 1.3 79.2 - - - +
175A ARG* 1.3 63.3 + - - +
177A GLU* 3.3 9.2 + - - +
178A ALA* 3.0 22.1 + - + +
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Residues in contact with ARG 175 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115A ASP* 3.5 13.5 + - - +
132A LEU* 2.8 41.9 - - - +
133A ALA 2.8 29.0 + - - +
134A ASP* 5.2 0.4 - - - +
135A ILE* 3.1 40.2 - - - +
160A VAL* 3.6 12.1 - - + -
162A ALA* 4.5 1.1 - - + +
171A GLU* 2.7 47.8 + - - +
172A ALA* 3.6 7.0 - - - +
174A LYS* 1.3 75.3 - - - +
176A ALA* 1.3 65.2 + - - +
178A ALA* 3.0 15.7 + - - +
179A TYR* 3.0 44.4 + - + +
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Residues in contact with ALA 176 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160A VAL* 3.6 10.2 - - + +
172A ALA 2.9 16.3 + - - +
173A LEU 3.7 2.2 - - - +
175A ARG* 1.3 76.5 - - - +
177A GLU* 1.3 57.5 + - - +
179A TYR* 3.3 1.0 + - - -
180A ARG* 2.9 31.2 + - - +
187A ILE* 3.5 24.1 - - + +
189A MET* 4.3 0.2 - - + -
202A PHE* 3.6 17.9 - - + -
206A TRP* 3.5 22.2 - - + -
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Residues in contact with GLU 177 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173A LEU* 3.1 37.1 + - - +
174A LYS* 3.6 7.4 - - - +
176A ALA* 1.3 78.4 - - - +
178A ALA* 1.3 61.6 + - - +
180A ARG* 3.9 3.2 - - - +
181A ASN* 3.0 38.5 + - - +
205A ALA 5.1 0.5 - - - +
206A TRP* 4.2 5.2 - - + -
209A GLN* 2.8 44.3 + - - +
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Residues in contact with ALA 178 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135A ILE* 3.5 31.0 - - + -
139A ALA* 4.1 8.2 - - + +
174A LYS* 3.0 12.0 + - + +
175A ARG 3.0 9.5 + - - +
177A GLU* 1.3 77.6 - - - +
179A TYR* 1.3 61.6 + - + +
181A ASN* 3.6 6.9 + - - +
182A ALA* 3.1 24.6 + - - +
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Residues in contact with TYR 179 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115A ASP* 2.8 36.3 + - - +
135A ILE* 3.9 29.7 - - + +
138A PHE* 3.3 30.8 - + + +
139A ALA* 4.1 8.7 - - - -
142A ILE* 3.9 5.6 - - + +
158A ALA* 3.6 32.1 - - + -
159A ARG 4.8 1.1 - - - -
160A VAL* 3.8 11.0 - - + -
175A ARG* 3.0 47.1 + - + +
176A ALA* 4.0 3.1 - - - +
178A ALA* 1.3 77.4 - - + +
180A ARG* 1.3 65.3 + - - +
181A ASN 3.2 0.4 - - - -
182A ALA* 3.1 13.5 + - - +
183A GLY 3.3 0.7 + - - -
184A ALA* 3.1 22.8 + - - +
187A ILE* 4.2 1.3 - - + -
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Residues in contact with ARG 180 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176A ALA 2.9 17.7 + - - +
177A GLU* 3.9 4.5 - - - +
179A TYR* 1.3 75.4 - - - +
181A ASN* 1.3 64.6 + - - +
183A GLY* 3.0 20.2 + - - -
184A ALA* 3.3 24.3 + - - -
185A ASP* 4.5 5.3 + - - +
186A ALA* 5.6 2.0 - - - +
187A ILE* 3.8 11.3 - - + +
206A TRP* 3.9 18.2 - - + -
209A GLN* 3.0 32.2 + - + +
210A GLY* 3.7 15.6 - - - -
211A PRO* 4.2 13.6 - - - +
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Residues in contact with ASN 181 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177A GLU* 3.0 30.3 + - - +
178A ALA* 3.8 6.1 - - - +
180A ARG* 1.3 83.3 - - - +
182A ALA* 1.3 56.4 + - - +
183A GLY* 3.0 4.2 + - - -
209A GLN* 5.5 4.3 + - - +
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Residues in contact with ALA 182 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139A ALA* 3.4 34.3 - - + +
142A ILE* 3.9 6.3 - - + +
143A LYS* 3.5 34.7 + - + +
146A LYS* 4.3 2.3 - - - +
178A ALA 3.1 16.0 + - - +
179A TYR* 3.4 13.0 - - - +
180A ARG 3.1 0.8 - - - -
181A ASN* 1.3 75.8 - - - +
183A GLY* 1.3 56.6 + - - +
184A ALA 3.7 0.4 - - - -
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il